This dissertation investigates the temporal and regional variation in human skeletal morphology in relation to climate and the environment in Holocene China. Linking skeletal morphology to the changes in climate, subsistence strategy and socio-political development has been well-documented in various geographical areas. Although a general pattern has been observed among different populations, it is evident that local factors have played an equally important role in human morphological variation. China was chosen in this dissertation because its diverse geographical, historical and cultural background provides an ideal setting in which to elucidate human biological responses to a variety different external forces and stimuli. A total sample of 533 adult skeletons, spanning from the mid-Neolithic to the twentieth century, was examined. These skeletons represent the ancient agriculturalists, nomadic pastoralists and agropastoralists inhabiting in contemporary Northeast China and modern humans from South China. This dissertation uses body size and shape, entheseal expression and biomechanical properties of long bones to investigate: 1.) temporal patterns in postcranial dimensions, stature and body mass; 2.) regional differences between the northern and southern Chinese in body size and body/limb proportions; and 3.) variation in skeletal biomechanics and entheses in relation to subsistence strategy. The findings in this dissertation indicated that while the human skeletons studied were morphologically varied throughout Holocene China, they were, to some extent, correlated with climatic and environmental factors. Body size and shape and body/limb proportions corresponded with variation in temperature. Additionally, stature, body mass and entheseal expression were correlated with socio-political and cultural development. Nevertheless, entheseal expression unexpectedly did not show a straightforward relationship with subsistence strategy, in which is inconsistent with the findings of previous studies. Although the comparisons of biomechanical properties were not unequivocal, they suggest differences in mobility and mechanical loading between different populations and subsistence strategies. On the whole, the results suggested that variation in skeletal morphology of the Holocene Chinese follows the universal patterns on the one hand, while on the other, they were influenced by local environmental and behavioural factors.

Temperate tree species exhibit seasonal growth cycling, and the timing of such transition varies with local climate. Under anthropogenic climate change, the local pattern of growth and dormancy in tree populations is expected to become uncoupled with shifting seasonal environmental signals, particularly temperature. Thus, an understanding of the genetic underpinnings of local adaptation is key to predicting the fate of tree populations in the future. In this thesis, we coupled sampling of range-wide natural accessions of P. trichocarpa with adaptive trait phenotyping and genome-wide genotyping to uncover relationships between genotype, phenotype, and environment. We detected strong correlations between adaptive phenotypes, climate, and geography, which suggested climatic selection driving adaptation of these populations to local environments. We subsequently combined genotype-phenotype association tests with sliding window analysis and identified regions strongly associated with these adaptive traits. We also compared adaptive markers identified in two independent GWAS on samples across latitude and altitude transects and found a set of associated variants shared across both transects. We further scanned the genome with three selection tests to identify regions showing evidence of recent positive and divergent selection. By comparing candidate selection regions across altitude and latitude, we detected a set of overlapping regions showing differentiation across gradients of the same climate variables. We validated the functional imortance of these selection regions by combining GWAS and showed that selection regions contain a strong signature of phenotypic associations. We also studied the distribution of deleterious allels across genome and natural populations, and found that deleterious alleles preferentially accumulate in regions of low recombination and hithihking regions. Finally, marginal populations contained more deleterious alleles compared with central populations, which is likely due to ineffective selection in small populations and recent bottlenecks associated with postglacial recolonization. These findings provide new insights into the genomic architecture underlying climatic adaptation and how selection drives adaptive evolution of tree species. / Ph. D.

Superior Ethmoidal Breadth (SEB = the maximum breadth between the left and right frontoethmoidal sutures) has been widely employed by anthropologists as a proxy for internal nasal airway dimensions since it is easily measured without imaging. SEB is also commonly argued to evince climatic adaption in modern humans, as populations living in cold-dry environments predictably exhibit narrower SEB dimensions than those inhabiting tropical environments. However, given uncertaintiy regarding its relationship with internal nasal anatomy, the accuracy of SEB as a proxy for airway dimensions remains questionable. Here, I evaluate the correlation between SEB and internal airway dimensions using linear measurements collected on CT scans from a mixed-sex sample of human crania (n=215) ancestrally derived from sub-Saharan Africa, the Arctic Circle, East Asia, and Europe. My results demonstrate that SEB is often located superior to the anatomcial roof of the nasal passages but is highly correlated (R= 0.8119, p<0.0001) with ethmoidal breadth taken at the functional level of the upper airways (i.e., functional airway breadth [FEB]). ANOVA results indicate, in addition to significant differences in SEB (χ2 = 82.20, p<0.0001), regional differences also exist for FEB (χ2 = 54.21, p<0.0001) and its components: the combined superior and superior common meatal breadths (χ2 = 19.03, p< 0.0001) and ethmoid air cell (EAC) breadth (χ2 = 27.67, p<0.0001). Further, following theoretrical expecations, the African-derived sample generally exhibits the widest internal nasal dimensions and the Arctic-derived sample the narrowest. Specifically, the Arctic sample exhibits significantly narrower airway breadths compared to all other groups. Conversely, the African sample possesses significantly wider EAC breadths comapred to all other groups. Cumulatively, these results empirically support use of SEB as proxy for upper nasal airway breadth and bolster claims that clinal variation in internal airway dimensions across human populations is likely attributable to climatic factors.

<p> As the effects of climate change become more evident, the development of effective strategies for improving livestock climatic adaptation and the long-term sustainability of animal food production have become key priorities around the world, including in the US. Together with nutrition, infrastructure, and management practices, genetically improving animals is an effective and lasting alternative to simultaneously improve productive efficiency and climatic adaptation of animals. Genetic improvement requires basic understanding of the genomic architecture of the indicator traits of interest and the availability of large-scale datasets. Understanding the role of evolution and selection (both natural and artificial) on shaping animal genomes is of paramount importance for the optimization of breeding programs and conservation of genetic resources. In addition, properly quantifying environmental stress and individual animal responses to thermal stress are still important challenges in breeding programs. Thus, the identification of optimal statistical methods and traits that better capture key biological mechanisms involved in the heat stress response has the potential to enable more accurate selection for thermal tolerant individuals. Therefore, this thesis aimed to investigate complementary topics related to thermal tolerance in livestock species based on genomic information. A total of 946 genotypes from 34 cattle breeds, as well as Datong yak (<em>Bos grunniens</em>) and Bali (<em>Bos javanicus</em>) populations, adapted to divergent climatic conditions, were used to investigate the genetic diversity and unravel genomic regions potentially under selection for thermal tolerance, with a focus on Chinese local cattle breeds and yak. Different signature of selection analyses and a comprehensive description of genetic diversity in 32 worldwide cattle and Datong yak populations was presented. Moderate genetic diversity was observed within each Chinese cattle population. However, these results highlighted the need to adopt strategies to avoid further reduction in the genetic diversity of these populations. Several candidate genes were identified as potentially under selection for thermal tolerance, and important biological pathways, molecular functions, and cellular components were identified, which contribute to our understanding of the genetic background of thermal tolerance in <em>Bos</em> species. Secondly, 8,992 genotyped individuals were used to provide a comprehensive description of genotype-by-environment interaction effects, defining optimal environmental variables based on public weather station data, and critical periods to evaluate heat tolerance for various reproduction, growth, and body composition traits in US Large White pigs. The period of 30 days before the measurement date was suggested to analyze genotype-by-environment interaction for off-test weight, muscle depth, and backfat thickness. While for number of piglets weaned and weaning weight, the suggested period ranged from the last trimester of gestation until weaning. This same population was used to access the genomic predictive ability of heat tolerance based on routinely-measured traits and explore candidate regions involved in the biological mechanisms that underlie heat stress response in pigs. Genotype-by-environment interaction was identified for most of the traits evaluated, and moderate (>0.36 ± 0.05) breeding values prediction accuracy were achieved using genomic information. Lastly, various behavioral, anatomical, and physiological indicators of heat stress were measured in a population of 1,645 multiparous Large White x Landrace lactating sows. This dataset was used to identify the best statistical models and estimate genomic-based genetic parameters for 23 indicators of heat stress, including automatically-measured vaginal temperature, skin surface temperatures, respiration efficiency, respiration rate, panting score, body condition scores, hair density, body size, and ear measurements. All the traits evaluated are heritable, with heritability estimates ranging from 0.04 ± 0.01 to 0.40 ± 0.09. The genetic correlations among these traits ranged from -0.49 (between repeated records of vaginal temperature measured at 0800 hours and caliper body condition score) to 1.0 (between repeated records of vaginal temperature measured at 0800 hours and single record of vaginal temperature measured at 0800 hours; and between repeated records of vaginal temperature measured at 1200 hours and single record of vaginal temperature measured at 1200 hours). These findings indicate that genetic progress for thermotolerance in pigs can be achieved through direct indicators of heat stress in selection schemes. However, special attention is needed due to complex relationship between these traits as evidenced by their genetic correlations. In conclusion, this thesis provides important information to be used when designing breeding strategies for improving thermal tolerance in cattle and pigs, important genomic regions and metabolic pathways that are important for understanding the biological mechanism regulating thermal tolerance, as well as future directions for investigations in the area of livestock climatic adaptation.</p>

Made available in DSpace on 2014-08-20T14:22:07Z (GMT). No. of bitstreams: 1 Tese_ Marcelo_ Couto.pdf: 11730472 bytes, checksum: afd142b8d56cb58f0be9327a636499ea (MD5) Previous issue date: 2006-11-27 / Insufficient chilling accumulation limits the production of peach in subtropical areas. Comparatively this combined with the wide temperature fluctuation during bud differentiation, through the bloom period and fruit growth and development may cause crop losses. Problems with low productivity in southern Rio Grande do Sul often attributed to the mild winter conditions, however, the environmental conditions especially around bloom period to be critical for optimal yields. In subtropical áreas temperature oscillations may cause problems during fertilization with subsequent reduction of fruit set and production instability of some peach cultivars. To better understand the effect of high temperatures on flower differentiation, pre-blooming, blooming, fruit set and fruit development and growth observations were made during the stages of bud differentiation, leafing and blooming, which included pollen production and viability, floral morphology, fruit set and the fruit growth and development. Temperature elevation with the tree was obtained by bagging branches with transparent plastic or with transparent plastic bottles. Plants of two low chilling peach cultivars (200 to 300 hours): Granada and Maciel were used in the years of 2003, 2004 and 2005. Conditions of high temperatures during the period of bud differentiation of Granada and Maciel did not promote the formation of double pistils or any morphologic anomalies. Bagging shoots with transparent plastic bags and plastic bottles is a simple and economical way of increasing the temperature on the branches under field conditions. High temperatures conditions during pre-blooming period advanced and accelerated the flowers anthesis and pistil growth. Flower morphology, regarding pistil length and weight, was not influenced by temperature elevation under experimental conditions. High temperatures during the pre-blooming negatively influenced the fruit set of the peach cultivar Granada. The percentage of in vitro pollen germination was different among cultivars and incubation temperatures. Pollen viability of cultivars Esmeralda, Granada, Jade and Maciel, can be evaluated by in vitro germination in standard culture medium (10% of sucrose + 1% of agar, dissolved in distilled water), three hours after the inoculation, with incubation at 24°C and 28°C. Under high temperatures conditions during the stage I of fruit growth and development of peach cultivars Granada and Maciel, cell division may be accelerated since a larger number of cells was counted in the pericarp tissue. / As horas de frio necessárias às gemas vegetativas e floríferas, quando insuficientes, limitam a produção de pessegueiros nas zonas subtropicais e temperadas brasileiras. A redução na produtividade pode ocorrer também, devido a variações bruscas na temperatura durante os períodos de diferenciação das gemas, préfloração, floração, crescimento e desenvolvimento dos frutos desta espécie. Estas variações de temperatura podem ser uma das causas da instabilidade produtiva de algumas cultivares de pessegueiro. Muito dos problemas que se verificam, após a floração ou mesmo na colheita, como baixa produtividade, atribuídos muitas vezes, apenas às condições de inverno com pouco frio que ocorrem no sul do Rio Grande do Sul, podem ter origem em etapa anterior do desenvolvimento e, muito provavelmente, na diferenciação floral. Com os objetivos de estudar a influência de altas temperaturas sobre diferenciação de gemas, pré-floração, floração, frutificação efetiva, crescimento e desenvolvimento de frutos, foram realizadas observações no avanço dos estádios de diferenciação das gemas, épocas de brotação e floração, testes de viabilidade e produção de pólen. Foram, ainda, feitas observações na morfologia e biologia floral, frutificação efetiva, crescimento e desenvolvimento dos frutos. A elevação da temperatura foi proporcionada com a utilização de casas de plástico ou através do ensacamento dos ramos com mangas de plástico transparente ou garrafas de plástico. Foram utilizadas plantas de duas cultivares comerciais de pessegueiro de baixa necessidade de frio (200 a 300 horas): Granada e Maciel em 2003, 2004 e 2005. Não há a formação de pistilos duplos ou quaisquer anomalias morfológicas mesmo sob temperaturas maiores que 25°C durante o período de diferenciação das gemas das cultivares de pessegueiro Granada e Maciel. Há diferenças entre cultivares e entre temperaturas de incubação quanto à porcentagem de germinação do pólen in vitro. A viabilidade do pólen das cultivares de pessegueiro testadas (Esmeralda, Granada, Jade e Maciel) pode ser avaliada por germinação in vitro em meio de cultura padrão (10% de sacarose + 1% de agar, dissolvidos em água destilada), três horas após a inoculação, com incubação a 24°C e 28°C. Ensacamento de ramos com plástico transparente ou com garrafas de plástico, é uma forma simples e econômica de aumentar a temperatura junto aos ramos das plantas, em condições de campo, sendo mais efetivo que o uso de estufas de plástico. Conclui-se que em condições de temperaturas elevadas, durante a pré-floração, ocorre a antecipação da antese das flores para as cultivares Granada e Maciel. A morfologia das flores, em relação ao comprimento e ao peso dos pistilos, não é influenciada pela elevação da temperatura nas condições experimentais utilizadas. Temperaturas elevadas durante a pré-floração, influenciam negativamente na frutificação efetiva da cultivar de pessegueiro Granada. Em condições de temperaturas, elevadas durante o estádio I de crescimento e desenvolvimento dos frutos, para as cultivares de pessegueiro Granada e Maciel, há uma tendência de formação de um maior número de células do pericarpo, o que ampliaria o potencial da produção de frutos com maior tamanho.

Abstract Both demographic histories and natural selection complicate the speciation process. There is a need to jointly study the effects of natural selection on so called magic traits that can cause reproductive isolation such as climatic adaptation, and its interaction with neutral demographic histories. Closely related incipient coniferous species offer us a great system for this effort. I used genetic variation at one set of climate-related candidate genes and another set of reference loci and cytoplasmic genomic fragments of two closely related parapatric pine species: Pinus massoniana Lamb. and Pinus hwangshanensis Hisa. Population genetic analyses were used to measure genetic variation and detect signals of ancient and recent selection. Speciation parameters including migration rates and divergence times at candidate genes and reference loci were compared under the Isolation with migration model. Hierarchical Approximate Bayesian Computation (ABC) was used to define demographic and speciation models. Intra- and interspecific genetic variation at cytoplasmic and nuclear intronic sequences were compared between parapatric populations and allopatric populations to distinguish the effects of introgression and incomplete lineage sorting in generating shared genetic variation between the species. The results showed that ancient selection were shared by the lineages leading to the species while recent selection has been species-specific. Candidate genes had significant lower migration rates compared to reference loci. Recent differential climatic selection might counteract against gene flow at underlying genes, which therefore favors divergence between the two pines through ecological speciation. Shared mitotypes were randomly distributed across species’ ranges, which therefore supported the incomplete lineage sorting hypothesis, but the shared nuclear intronic variation distributed more frequently in parapatric populations than in allopatric populations, supported the introgression hypothesis. ABC and species’ distribution modeling also supported the secondary gene flow model. The three genomes had different rates of mutation and gene flow might mirror different phases of the speciation continuum. The results in this thesis are valuable for understanding evolution in general and for other applied purposes such as tree breeding and climate change adaptation. / Tiivistelmä Luonnonvalinta ja populaatioiden historian demografia tekevät lajiutumisesta monimutkaisen tapahtumaketjun. Luonnonvalinnan ja demografisten tekijöiden vuorovaikutusta on paras tutkia samanaikaisesti, kun tarkastellaan lajiutumiseen vaikuttavia ominaisuuksia. Tällaisia ovat esimerkiksi ilmastoon sopeutumiseen liittyvät ominaisuudet. Lähisukuiset havupuulajit tarjoavat erinomaiset mahdollisuudet tähän työhön. Tutkin geneettistä muuntelua yhtäältä ilmastosopeutumiseen liittyvissä ns. ehdokasgeeneissä ja toisaalta neutraaleiksi oletetuissa verrokkigeeneissä sekä sytoplasman genomeissa kahdessa lähisukuisessa mäntylajissa Pinus massoniana Lamb. ja Pinus hwangshanensis Hisa, joiden populaatiot esiintyvät joskus erillään toisistaan (allopatrisesti), toisinaan vierekkäin (parapatrisesti). Mittasin muuntelun määrää ja etsin merkkejä valinnan vaikutuksesta. Vertasin erilaisia lajiutumismallien parametrejä verrokki- ja ehdokasgeeneissä. Käytin simulaatioita etsiäkseni parhaat demografiset ja lajiutumiseen liittyvät mallit. Vertasin kloroplastien ja mitokondrioiden genomien sekvenssien lajinsisäistä ja lajien välistä muuntelua allopatrisissa ja parapatrisissa populaatioissa tutkiakseni onko lajien yhteinen muuntelu seurausta siitä että lajien eriytymisestä on kulunut vain vähän aikaa vai siitä että sen jälkeen on tapahtunut geenivirtaa. Kauan sitten tapahtunut valinta on vaikuttanut samalla tavalla kumpaankin lajiin, osin koska tutkimus kohdistui myös niiden yhteiseen edeltäjälinjaan. Äskettäinen valinta taas oli suuremmassa määrin kummallekin lajille ominaista. Viime aikojen ilmastoon liittyvä valinta on voinut vähentää geenivirtaa ehdokasgeeneissä, mikä voisi edistää ekologista lajiutumista. Tuman DNA:n muuntelu jakautuminen tuki sitä mahdollisuutta että lajien yhteinen geneettinen muuntelu johtuu äskettäisestä geenivirrasta, ei vain siitä että lajiutuminen on niin varhaisessa vaiheessa. Mitokondrioiden geeneissä lajeilla yhtä paljon yhteistä muuntelua sekä allopatrisissa että parapatrisissa populaatioissa, mikä tukee sen sijaan eriytymisen jälkeistä epätäydellistä muuntelun erilaistumista. Eri genomit heijastavat lajiutumisprosessin eri vaiheita. Väitöskirjan tulokset ovat osaltaan tuottaneet uutta tietoa lajiutumisesta ja valinnasta. Lisäksi niillä on merkitystä ilmastomuutoksen vaikutusten ymmärtämisessä ja metsänjalostuksessa.